3B8H: EEF2-ExoA(E546A)-NAD+ complex

Structure of the eEF2-ExoA(E546A)-NAD+ complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 Jun 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Saccharomyces cerevisiae, Pseudomonas aeruginosa
Chains: 6
Atoms: 24,719
Mol. weight: 349.78 kDa
Ligands: NAD
Released: 17 Jun 2008

Explore 3B8H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B8H contains 176 α-helices and 185 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 43 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
α-helix	6-11	6
α-helix	16-18	3
β-strand	19-25	7	2
α-helix	28-30	3
α-helix	32-43	12
β-strand	44	1	2
β-strand	46-47	2	1
β-strand	70	1	3
β-strand	74-80	7	2
α-helix	83-88	6
β-strand	97-103	7	2
α-helix	112-120	9
β-strand	124-130	7	2
β-strand	134	1	2
α-helix	137-148	12
β-strand	152-158	7	2
α-helix	160-165	6
α-helix	171-192	22
α-helix	195-197	3
α-helix	204-206	3
β-strand	209-213	5	2
β-strand	218-221	4	2
α-helix	222-229	8
α-helix	237-243	7
β-strand	249-251	3	4
β-strand	256-258	3	4
β-strand	262	1	5
β-strand	268	1	5
β-strand	271	1	4
α-helix	272	1
α-helix	273-278	6
α-helix	279-289	11
α-helix	295-302	8
α-helix	309-313	5
α-helix	316-327	12
β-strand	329	1	2
α-helix	330-341	12
α-helix	343-344	2
α-helix	345-356	12
β-strand	357	1	6
α-helix	364-370	7
β-strand	379-387	9	7
β-strand	388	1	3
β-strand	394-402	9	7
β-strand	404-406	3	8
β-strand	410-414	5	7
β-strand	426-430	5	7
β-strand	433-438	6	7
β-strand	441-445	5	7
β-strand	447-449	3	8
β-strand	453-457	5	7
β-strand	467-470	4	7
α-helix	475-477	3
β-strand	478	1	6
β-strand	489-495	7	9
α-helix	501-514	14
β-strand	519-522	4	9
β-strand	528-532	5	9
α-helix	535-544	10
α-helix	545-549	5
β-strand	554-556	3	9
α-helix	557-559	3
β-strand	560-561	2	9
β-strand	564-567	4	10
β-strand	575-578	4	11
β-strand	585-592	8	11
α-helix	595-602	8
α-helix	612-623	12
α-helix	627-630	4
β-strand	633-636	4	11
β-strand	644-648	5	11
α-helix	656-659	4
α-helix	660-672	13
α-helix	679	1
β-strand	680-681	2	10
β-strand	684-692	9	11
α-helix	697-699	3
α-helix	702-719	18
β-strand	722-736	15	10
α-helix	737-739	3
α-helix	740-747	8
β-strand	753-759	7	10
β-strand	765-773	9	10
α-helix	774-776	3
α-helix	780-787	8
β-strand	793	1	10
β-strand	796-803	8	10
α-helix	814-826	13
α-helix	832-834	3
α-helix	835-838	4

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	408	1	12
β-strand	415	1	12
α-helix	419-431	13
β-strand	434-442	9	13
α-helix	444-453	10
α-helix	464-466	3
β-strand	469-471	3	14
β-strand	472	1	13
α-helix	475-479	5
β-strand	483	1	15
β-strand	495	1	15
β-strand	497-504	8	13
α-helix	505-510	6
β-strand	511-513	3	14
α-helix	517	1
α-helix	521-530	10
α-helix	534	1
α-helix	537	1
β-strand	541-545	5	14
β-strand	552-556	5	14
α-helix	558-561	4
β-strand	565-568	4	13
α-helix	571-573	3
α-helix	580-582	3
α-helix	584-586	3
α-helix	589-592	4
α-helix	596-600	5
β-strand	601	1	14

Chain C: 44 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	16
α-helix	6-14	9
α-helix	16-18	3
β-strand	19-25	7	17
α-helix	28-30	3
α-helix	32-43	12
β-strand	44	1	17
β-strand	46-47	2	16
β-strand	69	1	18
β-strand	70	1	19
β-strand	74-80	7	17
α-helix	85-88	4
β-strand	97-103	7	17
α-helix	112-120	9
β-strand	124-130	7	17
α-helix	137-148	12
α-helix	151	1
β-strand	152-158	7	17
α-helix	160-165	6
α-helix	171-192	22
α-helix	195-197	3
α-helix	204-206	3
β-strand	209-213	5	17
β-strand	218-221	4	17
α-helix	222-231	10
α-helix	237-243	7
β-strand	249-250	2	20
β-strand	257-258	2	20
β-strand	262	1	21
β-strand	268	1	21
β-strand	271	1	20
α-helix	272	1
α-helix	273-278	6
α-helix	279-287	9
α-helix	288-290	3
α-helix	296-302	7
α-helix	309-313	5
α-helix	317-327	11
β-strand	329	1	17
α-helix	330-341	12
α-helix	343-344	2
α-helix	345-356	12
β-strand	357	1	22
α-helix	364-370	7
β-strand	379-387	9	23
β-strand	388	1	19
β-strand	394-402	9	23
β-strand	404-406	3	24
β-strand	410-414	5	23
β-strand	426-430	5	23
β-strand	433-435	3	23
β-strand	438	1	18
β-strand	441	1	18
β-strand	444	1	23
β-strand	447-449	3	24
β-strand	453-457	5	23
β-strand	467-470	4	23
α-helix	475-477	3
β-strand	478	1	22
β-strand	489-492	4	25
β-strand	493-494	2	26
α-helix	502-514	13
β-strand	519-522	4	25
β-strand	528-532	5	25
α-helix	535-548	14
β-strand	555-556	2	26
α-helix	557-559	3
β-strand	560-561	2	25
β-strand	564-567	4	27
β-strand	575-578	4	28
β-strand	585-592	8	28
α-helix	593-594	2
α-helix	595-602	8
α-helix	612-623	12
α-helix	627-630	4
β-strand	633-636	4	28
β-strand	644-648	5	28
α-helix	656-659	4
α-helix	660-672	13
α-helix	679-680	2
β-strand	681	1	27
β-strand	684-692	9	28
α-helix	697-699	3
α-helix	702-718	17
β-strand	722-736	15	27
α-helix	740-747	8
β-strand	753-758	6	27
β-strand	765-773	9	27
α-helix	774-776	3
α-helix	780-787	8
β-strand	793	1	27
β-strand	796-803	8	27
α-helix	814-825	12
α-helix	832-834	3
α-helix	835-837	3

Chain D: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	408	1	29
β-strand	415	1	29
α-helix	419-430	12
β-strand	434-442	9	30
α-helix	444-451	8
α-helix	464-466	3
β-strand	469-471	3	31
β-strand	472	1	30
α-helix	475-479	5
β-strand	483	1	32
β-strand	495	1	32
β-strand	497-504	8	30
α-helix	505-510	6
β-strand	511-513	3	31
α-helix	521-531	11
α-helix	534	1
α-helix	537	1
β-strand	541-545	5	31
α-helix	550-551	2
β-strand	552-556	5	31
α-helix	558-561	4
β-strand	565-568	4	30
α-helix	571-573	3
α-helix	580-583	4
α-helix	584-586	3
α-helix	589-593	5
α-helix	596-600	5
β-strand	601	1	31

Chain E: 45 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	33
α-helix	6-14	9
α-helix	16-18	3
β-strand	19-26	8	34
α-helix	28-30	3
α-helix	32-43	12
β-strand	44	1	34
β-strand	46-47	2	33
β-strand	69	1	35
β-strand	70	1	36
β-strand	74-80	7	34
α-helix	85-88	4
β-strand	97-103	7	34
α-helix	109-111	3
α-helix	112-120	9
β-strand	124-130	7	34
α-helix	137-148	12
β-strand	152-158	7	34
α-helix	161-164	4
α-helix	171-181	11
α-helix	183-192	10
α-helix	204-206	3
β-strand	209-213	5	34
β-strand	218-221	4	34
α-helix	229-232	4
α-helix	237-244	8
β-strand	249-251	3	37
β-strand	256-258	3	37
β-strand	262	1	38
α-helix	267	1
β-strand	268	1	38
α-helix	269-270	2
β-strand	271	1	37
α-helix	272-273	2
α-helix	274-278	5
α-helix	279-289	11
α-helix	296-302	7
α-helix	317-327	11
β-strand	329	1	34
α-helix	330-340	11
α-helix	345-352	8
α-helix	354-356	3
α-helix	364-370	7
β-strand	379-387	9	35
β-strand	388	1	36
β-strand	394-400	7	35
β-strand	404-406	3	39
β-strand	410-414	5	35
β-strand	426-430	5	35
β-strand	433-438	6	35
β-strand	441-444	4	35
β-strand	447-449	3	39
β-strand	453-457	5	35
β-strand	467-470	4	35
β-strand	489-493	5	40
β-strand	494-495	2	41
α-helix	498-500	3
α-helix	501-511	11
β-strand	519-522	4	40
β-strand	528-532	5	40
α-helix	535-544	10
α-helix	545-549	5
β-strand	554-555	2	41
β-strand	560-561	2	40
α-helix	562	1
β-strand	564-567	4	42
β-strand	575-578	4	43
β-strand	585-592	8	43
α-helix	593-594	2
α-helix	595-602	8
α-helix	612-623	12
α-helix	627-630	4
β-strand	633-636	4	43
β-strand	644-648	5	43
α-helix	656-659	4
α-helix	660-672	13
α-helix	679	1
β-strand	680-681	2	42
β-strand	684-692	9	43
α-helix	697-699	3
α-helix	702-718	17
β-strand	722-736	15	42
α-helix	740-747	8
β-strand	753-759	7	42
β-strand	765-773	9	42
α-helix	774-776	3
α-helix	780-788	9
β-strand	793	1	42
β-strand	796-803	8	42
α-helix	814-826	13
α-helix	832-834	3
α-helix	835-837	3

Chain F: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	408	1	44
β-strand	415	1	44
α-helix	419-430	12
β-strand	434-442	9	45
α-helix	444-451	8
α-helix	464-466	3
β-strand	469-471	3	46
β-strand	472	1	45
α-helix	475-479	5
β-strand	483	1	47
β-strand	495	1	47
β-strand	497-504	8	45
α-helix	505-510	6
β-strand	511-513	3	46
α-helix	517	1
α-helix	521-531	11
α-helix	534	1
α-helix	537	1
β-strand	541-545	5	46
β-strand	552-556	5	46
α-helix	558-561	4
β-strand	565-568	4	45
α-helix	580-582	3
α-helix	584-586	3
α-helix	589-593	5
α-helix	596-598	3
β-strand	601	1	46

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor 2	A, C, E	protein	842	Saccharomyces cerevisiae	P32324 (AlphaFold model)
Exotoxin A	B, D, F	protein	207	Pseudomonas aeruginosa	P11439 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>3B8H_1 Elongation factor 2 (chains A, C, E)
MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTR
KDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALR
VTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFAR
TVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKM
MDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLL
EKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGP
ADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVP
GKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKV
MKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEI
CLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLA
IENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIK
DSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLA
DPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGF
TGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYD
KL

Sequence of entity 2 (B, D, F), FASTA

>3B8H_2 Exotoxin A (chains B, D, F)
AFLGDGGDVSFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRAR
SQDLDAIWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTSLTL
AAPEAAGEVERLIGHPLPLRLDAITGPAEEGGRLETILGWPLAERTVVIPSAIPTDPRNV
GGDLDPSSIPDKEQAISALPDYASQPG

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	3

Primary citation

The nature and character of the transition state for the ADP-ribosyltransferase reaction. Jorgensen, R., Wang, Y., Visschedyk, D. et al. EMBO Rep (2008) 9:802-809. DOI 10.1038/embor.2008.90 · PubMed

Other PDB entries of the same protein (UniProt P32324 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
1N0U 2.12 Å, Crystal structure of yeast elongation factor 2 in complex with sordarin
3B82 2.35 Å, Structure of the eEF2-ExoA(E546H)-NAD+ complex
3B78 2.5 Å, Structure of the eEF2-ExoA(R551H)-NAD+ complex
8EUB 2.52 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
1U2R 2.6 Å, Crystal Structure of ADP-ribosylated Ribosomal Translocase from Saccharomyces cerevisiae
8EVS 2.62 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8EVQ 2.72 Å, Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I
1ZM9 2.8 Å, Structure of eEF2-ETA in complex with PJ34
1N0V 2.85 Å, Crystal structure of elongation factor 2
8T3A 2.86 Å, Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry…
8EVR 2.87 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…

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